From 6c6cc414a50d6face858636745f8777067945b86 Mon Sep 17 00:00:00 2001 From: preecej Date: Fri, 12 Aug 2011 18:04:22 +0000 Subject: [PATCH] perldoc edits svn path=/; revision=152 --- preecej/perl_singletons/pathway_gene_swapper.pl | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/preecej/perl_singletons/pathway_gene_swapper.pl b/preecej/perl_singletons/pathway_gene_swapper.pl index c01ec1b..4c8e4a1 100644 --- a/preecej/perl_singletons/pathway_gene_swapper.pl +++ b/preecej/perl_singletons/pathway_gene_swapper.pl @@ -10,7 +10,7 @@ Pathway Gene Swapper =head1 DESCRIPTION -Swap out one set of genes (or gene representation) for another in an +Swap out one set of genes (or gene representations) for another in an existing PathVisio GPML file. Optionally removes literature references. If multiple replacement genes map to a single original gene, @@ -32,7 +32,7 @@ of cards). =head1 USAGE -pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE -v -G -d +pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE -L -v -G -d =head1 OPTIONS @@ -136,6 +136,7 @@ $Data::Dumper::Pad = "... "; # --------------------------------------------------------------------------- =item B +Accepts a config file path. Reads a configuration file and sets config values. Returns a hash with config values set. =cut @@ -355,7 +356,10 @@ sub show_input } # --------------------------------------------------------------------------- -=item B +=item B +Accepts a reference to a hash of existing hex ids and a string as +the "type" of ID (e.g. "Group.GraphId"). The latter is currently for +documentary purposes only. Generates a "random" 5-digit hexadecimal id, checks to see if it already exists in the hex list, and if not, adds it to the list of hex ids already present in the GPML doc. Otherwise, generates -- 2.34.1